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Setdb1 regulates Cohesin at H3K9me3-independent topological domains

ABSTRACT: Setdb1 regulates Cohesin at H3K9me3-independent topological domains

PROVIDER: PRJNA507948 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16938676_1.fastq.gz	Fastqsanger.gz
	SRR16938676_2.fastq.gz	Fastqsanger.gz
	SRR16938677_1.fastq.gz	Fastqsanger.gz
	SRR16938677_2.fastq.gz	Fastqsanger.gz
	SRR16938678_1.fastq.gz	Fastqsanger.gz

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Setdb1 regulates Cohesin at H3K9me3-independent topological domains [Hi-C]

Project description:Setdb1 regulates Cohesin at H3K9me3-independent topological domains [Hi-C]

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Setdb1 regulates Cohesin at H3K9me3-independent topological domains [ChIP-Seq]

Project description:Setdb1 regulates Cohesin at H3K9me3-independent topological domains [ChIP-Seq]

| PRJNA507949 | ENA

Setdb1 regulates Cohesin at H3K9me3-independent topological domains [RNA-Seq]

Project description:Setdb1 regulates Cohesin at H3K9me3-independent topological domains [RNA-Seq]

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Setdb1 regulates Cohesin at H3K9me3-independent topological domains [ChIP-Seq]

Project description:Identification of SMC1a and Setdb1 bound-loci in E14 mESCs.

2020-12-01 | GSE123244 | GEO

Setdb1 regulates Cohesin at H3K9me3-independent topological domains [RNA-Seq]

Project description:Identification of SMC1a and Setdb1 bound-loci in E14 mESCs.

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Setdb1 regulates Cohesin at H3K9me3-independent topological domains

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-12-01 | GSE123245 | GEO

Setdb1 regulates Cohesin at H3K9me3-independent topological domains [Hi-C]

Project description:Hi-C experiments were performed on E14 cells knocked down with shEV, shSetdb1, and shSmc1a. Please note that the GSM6037819 - GSM6037836 samples were generated with higher resolution to supplement the previous data (GSM5689250-GSM5689252) with low resolution.

2021-11-16 | GSE188753 | GEO

Cohesin causes replicative DNA damage by trapping DNA topological stress

Project description:DNA topological stress inhibits DNA replication fork (RF) progression and contributes to DNA replication stress. In Saccharomyces cerevisiae we demonstrate that centromeric DNA and the rDNA array are especially vulnerable to DNA topological stress during replication. The activity of the SMC complexes cohesin and condensin are linked to both the generation and repair of DNA topological stress linked damage in these regions. At cohesin enriched centromeres cohesin activity causes the accumulation of DNA damage, RF rotation and precatenation, confirming that cohesin dependent DNA topological stress impacts on normal replication progression. In contrast, at the rDNA cohesin and condensin activity inhibit the repair of damage caused by DNA topological stress. We propose that as well as generally acting to ensure faithful genetic inheritance, SMCs can disrupt genome stability by trapping DNA topological stress.

2020-03-03 | GSE131558 | GEO

Cohesin and CTCF Differentially Affect the Chromatin Architecture and Gene Expression in Human Cells

Project description:Recent studies of genome-wide chromatin interactions have revealed that the human genome is partitioned into many self-associating topological domains. The boundary sequences are enriched for binding sites of CTCF and the cohesin complex, implicating these two factors in the establishment or maintenance of topological domains. To determine the role of cohesin and CTCF in higher order chromatin architecture in human cells, we proteolytically cleaved the cohesin complex from interphase chromatin and examined changes in chromosomal organization as well as transcriptome. We observed a general loss of local chromosomal interactions upon disruption of cohesin complex, but the topological domains remain intact. However, we found that depletion of CTCF by RNA interference in these cells not only reduced intra-domain interactions but also increased inter-domain interactions. Further more, distinct groups of genes become mis-regulated upon depletion of cohesin and CTCF. Taken together, these observations suggest that CTCF and cohesin contribute in different ways to chromatin organization and gene regulation. Hi-C and mRNA-seq experiments in Cohesin and CTCF depleted HEK293 cells

2013-12-16 | E-GEOD-44267 | biostudies-arrayexpress

Cohesin is a key determinant of interphase chromosome domain architecture (HiC)

Project description:To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elements, suggesting that compartmentalization is important for genome function. Here we show that very specific long-range interactions are anchored by cohesin/CTCF sites, but not cohesin-only or CTCF-only sites, to form a hierarchy of chromosomal loops. These loops demarcate topological domains and form intricate internal structures within them. Post-mitotic nuclei deficient for functional cohesin exhibit global architectural changes associated with loss of cohesin/CTCF contacts and relaxation of topological domains. Transcriptional analysis shows that this cohesin-dependent perturbation of domain organization leads to widespread gene deregulation of both cohesin-bound and non-bound genes. Our data thereby support a role for cohesin in the global organization of domain structure and suggest that domains function to stabilize the transcriptional programs within them. Hi-C, ChIP-Seq and RNA-Seq experiments were conducted in mouse neural stem cells and mouse astrocytes

2013-12-11 | E-GEOD-49017 | biostudies-arrayexpress

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